If there was ever a prison that needed help, it was Limestone Correctional Facility.

Even within the troubled Alabama penal system, this state compound near Huntsville was notorious for cruel punishment and medical neglect. In one drafty, rat-infested warehouse once reserved for chain gangs, the state quarantined its male prisoners with H.I.V. and AIDS, until the extraordinary death toll - 36 inmates from 1999 to 2002 - moved inmates to sue and the government to promise change.

Alabama's solution was to fire the local company in charge of medical care and hire Prison Health Services, the nation's largest commercial provider of health care behind bars. Prison Health's solution was to recruit Dr. Valda M. Chijide, an infectious-disease specialist who arrived last November with a lofty title: statewide coordinator of inmate H.I.V. care.

She was an unlikely candidate for the job in one sense, having never stepped inside a prison. But it did not take her long to conclude that the chaos was continuing, and that much of the problem was Prison Health itself.

Though the company had promised the help of other doctors, she said, she was left alone to care for not only the 230 men in the H.I.V. unit, but the 1,800 other prisoners, too. Nurses were so poorly trained, Dr. Chijide said, that they neglected to hand out life-sustaining drugs or gave the wrong ones. Medical charts were a mess, she said, and often it was impossible to find such basic items as a thermometer, or even soap.

Dr. Chijide lasted barely three months. After she complained in writing, Prison Health suspended her for reasons it would not disclose, and she quit.

Her short, frantic stint - battling for drugs, hospitalizations and extra food for skeletal inmates, she said - was not unusual in the world of Prison Health Services, which has had a turbulent record in many of the 33 states where it has provided jail or prison medicine. But her story, a rare firsthand account of a doctor in charge of a prison's health care, offers an intimate glimpse of the company's work at a moment when the need for change could not have been more pressing, and the spotlight on Prison Health could hardly have been more intense.

Even then, interviews and the reports of a federal court monitor show, the state and the company made promises they did not keep, settling for care that jeopardized inmates' health. And Prison Health, which often laments the difficulty of finding qualified doctors to work in jails and prisons, searched nationwide for a specialist, only to question her integrity.

"If you bring up a problem that they don't want to hear about, they will attack you," said Dr. Chijide, 45. "I felt better resigning than staying on and bending my principles to their principles."

A Prison Health spokesman said the company "had great expectations" for Dr. Chijide (pronounced CHIJ-i-day), but was informed that she had violated company policy, though it would not say how. She was put on leave, the company said, and before it could investigate, she quit.

Dr. Chijide said the company never told her why it suspended her.

Executives said that Prison Health has greatly reduced the number of inmate deaths - to four during its nearly two years in Alabama - and made steady improvements in a difficult program that had been badly run for years. Its corporate medical director, Dr. Carl J. Keldie, said in an interview last December, while Dr. Chijide was still employed there, that the Limestone program was "excellent," and would eventually become one of the best in Prison Health's sprawling operations.

Around the nation, the company has drawn criticism from judges, government overseers, and whistle-blowers, and has paid millions of dollars in fines and settlements. In New York, state regulators have faulted Prison Health in several deaths, and are investigating whether it is even operating legally in the state. Yet the company has continued to grow, absorbing rivals and winning new contracts; its largest, serving New York City's jails, was renewed in January, as Dr. Chijide was lodging her complaints.

A low-key but tenacious woman who had a run-in with an earlier employer, Dr. Chijide says the care at Limestone was far from adequate, and there is evidence to support her. In February, the month she resigned, the court monitor described an H.I.V. unit riddled with rats, where broken windows had been replaced with plastic sheeting that was itself falling apart. Thousands of doses of prescribed medications had never been given, as far as the monitor could tell from the slapdash records. No one was being tested for tuberculosis or treated for hepatitis C, which prey on fragile immune systems.

Limestone is not the only hitch in Prison Health's effort to transform a penal backwater. Two hundred miles south, at the state's Julia Tutwiler Prison for Women, another federal monitor reported that Prison Health lacked any "organized and structured medical program," and deplored the care given two inmates who died last year.

There is, of course, a higher authority that Prison Health must answer to: the state official charged with making sure it lives up to its contract. That person is Ruth Naglich, who as associate commissioner of the Alabama Corrections Department is supposed to review the company's work.

Three years ago, Ms. Naglich was a Prison Health executive, vice president for sales and marketing, at the company's headquarters outside Nashville.

Ms. Naglich said her connections to the company helped her coax it to improve care. And though her department has moved to fine Prison Health $580,000 over the last year for failing to meet certain performance standards - the company is fighting the fines - she said, "I'm pleased with the progress they've made."

The progress required of the company is laid out in court documents; in their suit over the deaths at Limestone, inmates won a settlement in which the state - and, by extension, Prison Health - agreed in April 2004 to make dozens of fixes in the H.I.V. unit and allow the monitor to inspect regularly. The monitor's reports show the company has made advances in some areas but little headway on some of the most critical reforms, and at one point tried to cover up its failure to comply by hastily updating patient charts. In fact, Dr. Chijide said, the company never even told her about the court settlement.

The New York Times began asking Prison Health in April to discuss its work at Limestone. The company offered in June to arrange an interview with its president, Trey Hartman, but never made him available, and eventually answered only a small number of questions via e-mail.

"P.H.S. continues to provide evidence-based medical care to the patients of the A.D.O.C. in a timely and professional manner," said Benjamin S. Purser Jr., a spokesman for the company, referring to the Alabama Department of Corrections.

The company would not address the monitor's reports or the troubles Dr. Chijide said she had discovered.

"If I had known all those things," she said, "I never would have worked for them in the first place."

A History Kept Hidden

Ringed by corn and cotton fields, Limestone looks unremarkable, a collection of low-rise cellblocks crouched in the shadow of a watchtower. But it houses something unusual in the realm of corrections: a prison-within-a-prison where Alabama keeps all its male inmates with H.I.V. or AIDS, whether they are killers or petty thieves.

This unit was created in 1985 on the theory that segregation would curb infection and security risks - a notion that fell out of favor elsewhere, but not in Alabama, which says it is the only state that still quarantines them. Many corrections experts today say the practice actually increases the risk of infection, and invites neglect.

That is how it worked out at Limestone, according to inmates in the unit who filed suit in 2002, arguing that their living conditions and medical care, by a Birmingham company called Naphcare, amounted to a death sentence. The doctor they hired as a medical expert, Stephen R. Tabet, dug through the pile of mortality records - the rate of AIDS-related deaths in Alabama that year was more than twice the national prison average, according to the Justice Department - and assembled a gruesome gallery.

An emaciated 39-year-old wasted away after begging a doctor for sandwiches. A 29-year-old with pneumonia was short of breath when he arrived at the unit, but waited two days to see a doctor and get a prescription; he never received the medication, and on the fourth day, he suffocated. A 41-year-old, also struggling to breathe, was sent off to a hospital two hours away in a prison van with no medical help, even after a guard urged that he be rushed in an ambulance. "He'll be fine," a nurse said, but the man had a heart attack on the way and died.

Treatment was not much better for those who survived. Packed into bunks so close that infectious abscesses "spread like wildfire," Dr. Tabet wrote, they were rousted at 3 a.m. to stand in line outdoors, often in the cold or rain, to get their pills.

Naphcare defended its record in a statement, but conceded that many deaths might have been prevented. It blamed the state for limits on food, shelter and medical services.

The state dropped Naphcare and hired Prison Health Services in November 2003, under a three-year, $142.7 million contract for all Alabama prisons. And in April 2004, the 18-page settlement of the inmate lawsuit was hailed as the blueprint the state and company would use to bring the unit into the 21st century. The old warehouse had been replaced by two cellblocks; in another change, prisoners would no longer have to pack dead cellmates into body bags.

The big moment, however, came last November, when Prison Health hired the H.I.V. specialist who would lead the charge: Dr. Chijide, who had answered the company's help-wanted ad in a medical journal.

Though she lacked prison experience, she did not shrink from a challenge, once spending seven years treating native people in Alaska. She also had grown up in Alabama, so moving back with her husband and two daughters would be a homecoming.

The company offered her $180,000 a year and told her, she said, that she could set her own treatment program and hours. She would be assisted by the prison's medical director and another full-time doctor, she said, along with a nurse assigned to the unit.

But the medical director quit, and Prison Health never produced the other help. It did not give Dr. Chijide any orientation, she said, or the written policies and procedures essential to any prison clinic. The only prison training she got was a week in a California prison AIDS clinic run by the expert monitoring the settlement.

Dr. Chijide said Prison Health never mentioned the terms of the settlement and the obligation it placed on the company. It was the court monitor himself, Dr. Joseph Bick, who suggested she look up the lawsuit on the Internet. Returning home from his clinic, she entered the prison's name on Google and found the horrifying death reports.

"Wow," she recalled thinking. "So this is what's going on."

Running on Empty

The inmate complained of chest pains, so Dr. Chijide sent him to the prison infirmary. But when she checked in on him, she said, he was holding a bottle of nitroglycerin pills that a nurse had handed him, to take as he liked. The nurse was nowhere to be found.

Nurses, she discovered, were prescribing drugs and making diagnoses without her consent. "I found cases where nurses had written 'verbal orders, Dr. Chijide' when I hadn't prescribed anything," she said. Yet her own prescriptions often went unheeded; the antibiotics she ordered for an inmate with perilously weak immunity were found days later on a medicine cart.

Lab-test results were lost or ignored, she said. A rat scuttled through her examination room. Inmates, assigned to the H.I.V. unit without any notice from prison officials, simply showed up unannounced. "Nobody said to me, 'These inmates have arrived; you need to see them,' " she said. So she asked nurses whether they had noticed any new faces, or went searching herself.

The prison medical director, Dr. Wyndol S. Hamer, resigned in early December, a few weeks after Dr. Chijide started. The company said his decision was personal, and Dr. Hamer - who Dr. Chijide said had criticized Prison Health during staff meetings - would not comment.

Whatever the reason, his departure left Dr. Chijide the only physician for all of Limestone. Each day became a race to treat inmates in the infirmary, answer sick calls and hunt down missing medical records. The H.I.V. unit had no clerical help, and the prison had no computer system to track patients, she said, so those records were often little more than notes on scraps of paper.

No patients died under her care, Dr. Chijide reflected with relief. But she felt she had merely been lucky.

When an inmate in the unit contracted tuberculosis in January 2004, before she arrived, Prison Health had to put all 230 prisoners, and several guards, on drugs for nine months to prevent the disease from spreading, Dr. Chijide said. Yet nearly a year later, she said, the unit still had no place to quarantine inmates with TB or hepatitis C.

Appeals for anything beyond the routine - treatment at outside hospitals, prescriptions not in the company pharmacy - became tangled in delays and denials, she said. And the dearth of everyday supplies, she said, ventured toward the absurd.

Sometimes, she said, she was forced to write "no thermometer" on a patient's chart - if there was a chart at all. Often, discovering that soap dispensers were empty in the infirmary, where the sickest prisoners were kept, she had to pause between patients and walk to the prison pharmacy, or to a bathroom at the other end of the building. "I had never been in a hospital or clinic that didn't have soap or paper towels," she said.

But, Dr. Chijide said she learned at last, the Prison Health operation was not like any other. "Nobody was really making an effort to run an H.I.V. clinic the way it was supposed to," she said. "They would tell you one thing, but when it came down to it, they didn't provide the resources."

A Reckoning, and a Warning

She was not shy about speaking up. When her complaints drew no response, she started taking notes. And on Christmas Day, her first real break, she laid out her grievances in a 10-page letter to the company.

Dr. Chijide had fought this sort of battle before. In 1993 she sued the Alaska clinic, saying that it had given her an unreasonable schedule and improperly ended her contract. A state court ruled that she had been let go without proper notice, but the Alaska Supreme Court reversed the decision.

This time, she had added backing: the reports of the court monitor, Dr. Bick.

On Jan. 20, nearly a month after her letter, two Prison Health executives sat her down. The timing was significant: Dr. Bick was to return in 18 days. The company had been at the prison well over a year.

Dr. Chijide said the executives blamed her for the unit's troubles, accusing her of seeing too few patients, coming and going as she pleased, and documenting too many problems. If the monitor found Prison Health out of compliance with the settlement, she said they told her, it would not be good for the company - or her.

Undeterred, Dr. Chijide wrote to them again, saying she had been scapegoated. Prison Health suspended her, but prepared for the inspection by granting some of the things she had asked for, including a nurse. The prison staff set out fresh rat traps.

And with Dr. Chijide gone and the monitor about to arrive, a Prison Health doctor raced through more than 100 medical charts in two or three days, jotting notes to make it appear that prisoners had received proper physical examinations.

The monitor was not fooled. "Patients allege that this physician spent a few minutes with each of them, did not touch them, did not answer questions, and rarely looked up from his writing," he wrote. The company's last-minute efforts, he said, "do not meet any reasonable standard of H.I.V. care."

In an interview, Dr. Bick was reluctant to go beyond the statements in his reports, which have commended Prison Health for keeping better records and for stopping nurses from acting beyond the scope of their licenses. He said he believed that the company intended to live up to the settlement, but "you can't be successful when you're trying to hide your warts and not rising to the challenges that you face."

Prompted by his findings, the Southern Center for Human Rights, which filed the original inmate lawsuit, asked a federal judge to hold the company in contempt for violating the settlement; he has not ruled. Human Rights Watch asked Gov. Bob Riley of Alabama to take immediate action to ensure the state's compliance; a spokesman for the governor would not comment.

Dr. Chijide has accepted a job at a Canadian hospital. But she says she still worries about Limestone's fate under Prison Health Services. "They were the type of people who were going to run the facility any way they want," she said. "And they were going to save money any way they can."

On July 1, Prison Health said, it filled her job. But in a report five days earlier, Dr. Bick warned that "the rapid turnover" of doctors was a dangerous problem. He urged the company to stop it.

"Due to the fragile nature of this medical program," he wrote, "I recommend that every effort be made to retain physicians once they are hired."

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